The profiler software isn't THAT bad. It just needs each profile linked to the .exe of the game associated with it. So you may want to duplicate a small rarely used .exe a load of times so you can have multiple profiles for dcs.
You can either link the profile to the exe so it loads the correct profile at game startup, or set the profile manually. Manual is the only option for DCS really as you want a profile per aircraft.
Another minor issue with the profiler is that the mode switch tends to reset to 1 whenever you add a new command. So if you create the key command when you go to bind it it will usually need resetting again as it will have defaulted to mode 1. Ideally set up your commands 1st, then allocate them to buttons.
Other things to consider: Update to the latest firmware for the stick. This eliminates the reversal bug on the X and Y axis.
Set "hysteresis" options to minimum via "game controllers" "properties" in windows. This will minimise the reversal bug for the other axis.
Finally to completely eliminate the reversal bug you will need to run the axis through a seperate USB controller board like one from Leo Bodnar. This is a relatively big job though requiring you to open up the rudder pedals and throttle and replace wires + extend them outside of the casings.